Hi Tsjerk

Now it DOES change the color of the inside of helixes. Thank you so much.

I think this is what happened. I was using the preset publication command to generate cartoons and then changing things. Once preset publication is invoked the command set cartoon_highlight_color, blue does not change anything. When I tried to use what you suggested on the same file (set cartoon_highlight_color, blue, helix A) it changed the color for the whole molecule, not just helix A.

So I started with a fresh pdb file and now it seems that by default pymol colors the inside and outside of the helix the same. And when I make selections and change colors for that selection, the changes including the colors of the inside of the helix are confined to that selection.

Thank you again, it was driving me nuts.

sdat5885



On Mon, Aug 16, 2010 at 12:54 AM, Tsjerk Wassenaar <tsjerkw@gmail.com> wrote:
Hi Sdat5885,

Have you started a fresh session, or did you a. load a session file or
b. did some other things you didn't mention before? It may be that you
have specifically set the highlight color for your protein. The
default is not grey, but whatever color the C alpha atom has. You
might want to  try:

set cartoon_highlight_color, blue, object_to_highlight

Cheers,

Tsjerk

On Mon, Aug 16, 2010 at 6:49 AM, s dat <sdat5885@gmail.com> wrote:
> Hi Jason
>
> Sorry but it does not work. The version is PyMOL 0.99rc6, OS is XP
> Professional 2002 SP3.
>
> Thanks for the help,
> Sdat5885
>
> On Sun, Aug 15, 2010 at 6:44 PM, Jason Vertrees
> <jason.vertrees@schrodinger.com> wrote:
>>
>> Vitaly is right,
>>
>>    "set cartoon_highlight_color, blue"
>>
>> will set the inside helical color to blue.  If you're having problems,
>> please let us know which version of PyMOL you're using and on which OS
>> (including version).
>>
>> Cheers,
>>
>> -- Jason
>>
>> On Sun, Aug 15, 2010 at 1:26 AM, s dat <sdat5885@gmail.com> wrote:
>> > Dear All
>> >
>> > set cartoon_highlight_color, blue does not change anything in my figure.
>> > If
>> > I the type set cartoon_highlight_color, -1 I get the following message:
>> >  Setting: cartoon_highlight_color set to default.
>> >
>> > The default right now is grey. I tried to go into settings, change the
>> > default to for ex blue, and then tried to recolor but nothing happened !
>> >
>> > Thanks
>> > sdat5885
>> >
>> > On Sat, Aug 14, 2010 at 9:40 PM, Vitaly Vostrikov <vvostri@uark.edu>
>> > wrote:
>> >>
>> >> Hello,
>> >>
>> >> I think this is the correct syntax:
>> >> set cartoon_highlight_color, blue
>> >>
>> >>
>> >> Vitaly
>> >>
>> >> ----- Original Message -----
>> >> From: s dat <sdat5885@gmail.com>
>> >> Date: Saturday, August 14, 2010 11:08 pm
>> >> Subject: [PyMOL] Newbie question : what command to use for changing
>> >> color
>> >> of inside of helix
>> >> To: pymol-users@lists.sourceforge.net
>> >>
>> >> > Dear All
>> >> >
>> >> > The default setting for color of inside of helices is grey. I am
>> >> > trying to
>> >> > color helices the same, both inside and outside. I tried using
>> >> > cartoon_highlight_color, blue but that does not change the grey to
>> >> > blue. Any
>> >> > help would be greatly appreciated.
>> >> >
>> >> > Thanks
>> >> > sdat5885
>> >> >
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > This SF.net email is sponsored by
>> >
>> > Make an app they can't live without
>> > Enter the BlackBerry Developer Challenge
>> > http://p.sf.net/sfu/RIM-dev2dev
>> > _______________________________________________
>> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
>> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
>> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> >
>>
>>
>>
>> --
>> Jason Vertrees, PhD
>> PyMOL Product Manager
>> Schrodinger, LLC
>>
>> (e) Jason.Vertrees@schrodinger.com
>> (o) +1 (603) 374-7120
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
> _______________________________________________
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>



--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands